Evaluating Neanderthal genetics and phylogeny

Ancient mitogenomics

The mitochondrial genome has been the traditional focus of most research into ancient DNA, owing to its high copy number and population-level variability. Despite this long-standing interest in mitochondrial DNA, it was only in 2001 that the first complete ancient mitogenomic sequences were obtained. As a result of various methodological developments, including the introduction of high-throughput sequencing techniques, the total number of ancient mitogenome sequences has increased rapidly over the past few years. In this review, we present a brief history of ancient mitogenomics and describe the technical challenges that face researchers in the field. We catalogue the diverse sequencing methods and source materials used to obtain ancient mitogenomic sequences, summarise the associated genetic and phylogenetic studies that have been conducted, and evaluate the future prospects of the field.

Phylogeographic distribution of mitochondrial DNA macrohaplogroup M in India

Indian subcontinent harbours both the human mtDNA macrohaplogroups M and N, of which M is the most prevalent. In this study, we discuss the overall distribution of the various haplogroups and sub-haplogroups of M among the different castes and tribes to understand their diverse pattern with respect to geographical location and linguistic affiliation of the populations. An overview of about 170 studied populations, belonging to four distinct linguistic families and inhabiting different geographic zones, revealed wide diversity of about 22 major haplogroups of M. The tribal populations belonging to the same linguistic family but inhabiting different geographical regions (Dravidian and Austro-Asiatic speakers) exhibited differences in their haplogroup diversity. The northern and southern region castes showed greater diversity than the castes of other regions.

To what extent did Neanderthals and modern humans interact?

Neanderthals represent an extinct hominid lineage that existed in Europe and Asia for nearly 400,000 years. They thrived in these regions for much of this time, but declined in numbers and went extinct around 30,000 years ago. Interestingly, their disappearance occurred subsequent to the arrival of modern humans into these areas, which has prompted some to argue that Neanderthals were displaced by better suited and more adaptable modern humans. Still others have postulated that Neanderthals were assimilated into the gene pool of modern humans by admixture. Until relatively recently, conclusions about the relationships between Neanderthals and contemporary humans were based solely upon evidence left behind in the fossil and archaeological records. However, in the last decade, we have witnessed the introduction of metagenomic analyses, which have provided novel tools with which to study the levels of genetic interactions between this fascinating Homo lineage and modern humans. Were Neanderthals replaced by contemporary humans through dramatic extinction resulting from competition and/or hostility or through admixture? Were Neanderthals and modern humans two independent, genetically unique species or were they a single species, capable of producing fertile offspring? Here, we review the current anthropological, archaeological and genetic data, which shed some light on these questions and provide insight into the exact nature of the relationships between these two groups of humans.

Mitochondrial DNA evidence for a diversified origin of workers building First Emperor of China

Variant studies on ancient DNA have attempted to reveal individual origin. Here, based on cloning sequencing and polymerase chain reaction-restriction fragment length polymorphisms, we analyzed polymorphisms in the first hypervariable region and coding regions of mitochondrial DNA of 19 human bone remains which were excavated from a tomb near the Terra Cotta Warriors and dated some 2,200 years before present. With the aim of shedding light on origins of these samples who were supposed to be workers building the mausoleum for the First Emperor of China, we compared them with 2,164 mtDNA profiles from 32 contemporary Chinese populations at both population and individual levels. Our results showed that mausoleum-building workers may be derived from very diverse sources of origin.

Can identification of a fourth domain of life be made from sequence data alone, and could it be done on Mars?

A central question in astrobiology is whether life exists elsewhere in the universe. If so, is it related to Earth life? Technologies exist that enable identification of DNA- or RNA-based microbial life directly from environmental samples here on Earth. Such technologies could, in principle, be applied to the search for life elsewhere; indeed, efforts are underway to initiate such a search. However, surveying for nucleic acid-based life on other planets, if attempted, must be carried out with caution, owing to the risk of contamination by Earth-based life. Here we argue that the null hypothesis must be that any DNA discovered and sequenced from samples taken elsewhere in the universe are Earth-based contaminants. Experience from studies of low-biomass ancient DNA demonstrates that some results, by their very nature, will not enable complete rejection of the null hypothesis. In terms of eliminating contamination as an explanation of the data, there may be value in identification of sequences that lie outside the known diversity of the three domains of life. We therefore have examined whether a fourth domain could be readily identified from environmental DNA sequence data alone. We concluded that, even on Earth, this would be far from trivial, and we illustrate this point by way of examples drawn from the literature. Overall, our conclusions do not bode well for planned PCR-based surveys for life on Mars, and we argue that other independent biosignatures will be essential in corroborating any claims for the presence of life based on nucleic acid sequences.